how to extract content from dbSNP database using set of "rsid's".

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3.1 years ago

deepak.deucy ▴ 10

I have a list of 1000 "rsid's". I am trying to get information related to those id's from the dbSNP database, my main concern is to get info about NMID, chromosome start, end position information onto a text document or excel file. If someone has already had a similar script related to this type of content extraction, it would be really helpful if you provide a link to that or just provide some guidance on how to go about this task.

dbSNP rsid dataretrieval database snp • 1.5k views

ADD COMMENT • link 3.1 years ago by deepak.deucy ▴ 10

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what is 'nmid' ?

ADD REPLY • link 3.1 years ago by Pierre Lindenbaum 161k

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It is a reference ID from NCBI, it's an important variant ID, rsid's keeps changing but once assigned NMID won't change.

ADD REPLY • link 3.1 years ago by deepak.deucy ▴ 10

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okay... so where can I find the nmid for this snp #rs25 for example ? https://www.ncbi.nlm.nih.gov/snp/rs25

ADD REPLY • link 3.1 years ago by Pierre Lindenbaum 161k

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i have highlighted it

ADD REPLY • link 3.1 years ago by deepak.deucy ▴ 10

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I have highlighted NMID on the result page provided for the rsid mentioned by you enter image description here

ADD REPLY • link 3.1 years ago by deepak.deucy ▴ 10

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this is not a 'nmid', NM_015204.3 is a refseq indentifier fo the transcript where rs25 is mapped. https://www.ncbi.nlm.nih.gov/nuccore/NM_015204.3

Homo sapiens thrombospondin type 1 domain containing 7A (THSD7A), mRNA

ADD REPLY • link 3.1 years ago by Pierre Lindenbaum 161k

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yes, NM_015204.3 similar to this, RefSeq identifier for the transcript where "rsid's" of interest are mapped, I need that.

ADD REPLY • link 3.1 years ago by deepak.deucy ▴ 10

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